On this page we will look at how the nucleotides (the ones with one
phosphate group) bond to one another to form nucleic acids.
|For reasons that will soon become obvious, I'm going to make several
changes in the way that I have represented the structure here. (One is to add that oxygen
that I had inadvertently left out before.) Another is to rotate the phosphate. Also,
instead of writing out the structure of the base, I will just write "base" and
change the angle a little bit.
Again, keep in mind that this is a two-dimensional
drawing, so it really doesn't represent the actual shape of this molecule.
|The nucleotides bond to one another in a sequence of catalyzed dehydration
reactions. One OH group on the phosphate and the OH
group on the third carbon of the sugar are the functional groups which allow for the
polymerization of the nucleotides into a polynucleotide or nucleic acid.
|Note that the phosphate group links the third carbon of
one sugar molecule to the fifth carbon of the next sugar molecule.
Because of that, this can be called a 3'-5' phosphate ester link (or a 3'-5'
phospho diester link, pronounced 3-prime, 5-prime (3'-5') phospho diester). The
carbon atoms in the ribose portion of a nucleotide are numbered with primes (1', 2', 3',
4', 5') to distinguish them from the carbon and nitrogen atoms in the base which are
numbered without primes.
You may have wondered (as I did when I first learned about DNA and RNA) why these
chemicals are called nucleic acids if they are made up of bases.
Well, it's the hydrogen that still remains on the phosphate group from the phosphoric acid
that is acidic and gives these nucleic acids their acidic nature and thus, their name,
nucleic acids. Because these hydrogens are acidic, they can come off and when they do so,
they would leave behind a negative charge on the nucleic acid molecule. (At that point you
actually have the conjugate base of the nucleic acid.) Depending on the references that
you work with, you may see these molecules written with the hydrogens on (as shown above)
or with the hydrogens removed and a negative sign in their place. Undoubtably, at
biological pH, an equilibriium exists and both forms are present.
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